IMHO The rejected design is more ... well ... heraldic whereas the adopted design reminds me of one of those pseudo heraldic war gamer site logos designed by a 21 year old who still thinks like a 13 year old boy.

To me the choice represents the triumph of Arab-style armorial-type symbolism (not armorial per se) over something more African. The first design has a good deal in common with the arms of Kenya, Uganda and Tanzania.This is ironic, considering that the existence of South Sudan is in essence a rejection of Arab/Muslim control.